Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28

Non-O157 Shiga Toxin-Producing Escherichia coli − a Poorly Appreciated Enteric Pathogen: Systematic Review

(2018) Evangelia Valilis et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits

(2015) Michelle Qiu Carter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7

(2014) Kerry K Cooper et al.   BMC GENOMICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Multistate Outbreak of Escherichia coli O145 Infections Associated with Romaine Lettuce Consumption, 2010

(2013) E. V. TAYLOR et al.   JOURNAL OF FOOD PROTECTION

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Importance of prophages to evolution and virulence of bacterial pathogens

(2013) Louis-Charles Fortier et al.   Virulence

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Multicenter Evaluation of a Sequence-Based Protocol for Subtyping Shiga Toxins and Standardizing Stx Nomenclature

(2012) F. Scheutz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Shiga toxin in enterohemorrhagic E.coli: regulation and novel anti-virulence strategies

(2012) Alline R. Pacheco et al.   Frontiers in Cellular and Infection Microbiology

The complete DNA sequence and analysis of the virulence plasmid and of five additional plasmids carried by Shiga toxin-producing Escherichia coli O26:H11 strain H30☆

(2011) Pina M. Fratamico et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Genomic anatomy of Escherichia coli O157:H7 outbreaks

(2011) M. Eppinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role and clinical course of verotoxigenic Escherichia coli infections in childhood acute diarrhoea in Argentina

(2009) M. A. Rivero et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Pathogenomics of the Virulence Plasmids of Escherichia coli

(2009) T. J. Johnson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

(2009) Y. Ogura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Defective Prophage Pool of Escherichia coli O157: Prophage–Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants

(2009) Md Asadulghani et al.   PLoS Pathogens